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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgcgcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT

Basic information

species Zea mays
transcript GRMZM2G040924_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g42870.1 (Oryza sativa), 3'ss of exon 1
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgcgcggtctcatctaaccccca-ttcgcggcgcatt---tgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
                                                                                            |   | |       | |   |   ||  | |  |  || |  |   ||   |        | ||  |||||      || ||||    || ||   ||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||
--------------------------------------------------------------------------------------------ctctcttttcgtgcatgagaagtact-cggtattattcacaggagctgagagactctagtccgttccatctggataacacttcgttttgcgttgcatgcagGGCTGAACCGGTGCGGCAAGAGCTGCCGGCTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACCGCCGAGGAGCAGAAGTCCAT

upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttag--ttctgcagctgcctccctgccggcct-caaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgcgcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
                                                                    |||||   |||  || |   ||| || |  | |  ||   | ||   ||| ||| |||  |         ||||| |  |     ||       ||  |||| ||||| |      | ||  ||| ||    || || || |||||||| || ||||||||||||||||| || || || ||||| ||||| |||||||| ||  | || ||  |||   ||||
--------------------------------------------------------------------gttaggtctctaaagattgatccttggcaacttgtaaatgttcg---acgcctgggattttat-------gattgaaaactttaacg-------attgaaccaccatttg-----aactt--agGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT

upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S1_78V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtg-atgcttctcgct-cggattgcaggcacacgcgcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
                                                       ||    || | |    |       |   |  |   ||  ||     |    |  | | ||  | |  ||  || |||   ||| || |   |   |   |  |||    | |     |||    | | | || |||| ||  | || || ||||||||||| ||| |||||||||||||||||||  |||||||||||||||| || |  ||| ||   |||||| |  ||   ||
-----------------------------------------------------gtacatattcattt--gcaaccggataagcgagtag-tgatggagcagaatgcattggttcgtttctacatttttatcgaaacggctttctttctttctttctttctttctttattt--atttcttgtgaaatt-cagGCCTTCAGCGTTGTGGCAAGAGCTGTCGATTGCGGTGGACGAACTACCTTAGGCCGGACATCAAGCGAGGTCGATTCTCACAAGAGGAGGACCAGATGAT

upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S2_55V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgcgcggtctcatctaacccccattcg--cggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCAC---ATCCGAGGAGCAGAAGTCCAT
                                                     |  |     | |||| ||  ||||  | || |  |   | ||  |  |    |    ||     |  | || ||     |||||  |  |  |         | | ||          |  |   ||  ||| |||||| || |   |||| |||||||||||  || || | |||||||||||| | ||||| |||||||||||||| |  ||| |   | | ||||| |||| |     
---------------------------------------------------gtaggcatgaacctcttttttcttctaaaacttcaacaacgtcgtgcatagaagtc---atctaagttcggtgatttcacatcggagcggcgcgattgatcgaatttaatggcgtgtgtgtatggctggaacatgtgcagGTCTGATGAGGTGTGGCAAGAGCTGTAGATTGAGATGGACGAACTACTTGCGGCCCGACATCAAGCGCGGCCGTTTCTCCGAAGCTGAGGATCAGATGAT---

upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S45_150V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgc--gcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
                                           ||   ||| |||| |  |  |       | |  ||  |  |  |     |         || |     |   | | |  |  ||||| |     |   | |   |        || |     |    || || |   || | | ||||||||  | || || || |||||||| ||| || ||||||||||||||||  |||||||||||||||| || |  ||| ||   |||||| |  ||   ||
---------------------------------------gtaagtggtcactcacaagtggatgagcgtgcactgttgttgtagtgtatacact--------ccgtttttgtttagttttattttttctctcctccttgataagtgtagcttgaaagtgttgatcagtttcc-ttggttacgaaat-gcagGGCTCCAGCGATGTGGTAAGAGCTGTCGATTGAGGTGGACGAACTACCTAAGGCCGGACATCAAGCGAGGTCGATTCTCACAGGAGGAGGACCAGATGAT

upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S326_37V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgcgcggtctcatct--aacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
                                                                                           | | |    | | ||  | ||   |   || | |    ||      | |           || ||| |||    |   | ||||          || |||||||     ||||||||||||||||  | ||||||||||||||||| ||  | || ||||||||||| || |  ||| |   ||||||| |  ||   ||
---------------------------------------------------------------------------------------aatgggcagtgagatcaatg-gaattgagtcatgtttcagggcgacaaagtagagtttctgtctgcagtcccattctgagtgcgcatttttt---ttctttcagGGCTTGCGAGGTGCGGCAAGAGCTGTAGGCTGCGGTGGACGAACTATCTGAGACCTGACATCAAGCGAGGACGATTCTCTCACGAGGAGGACCAGATGAT

upper sequence: GRMZM2G040924_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ18723 (Selaginella moellendorffii), 3'ss of exon 1
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacg-cgcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
                                                                                                                                      | || |    | |||  |   |||||||   |    |  | |   |      ||||| || || || ||||||||||| ||| | ||||| ||||||||||| ||||||||||| || || || ||     ||||| || | ||  ||| || |  
------------------------------------------------------------------------------------------------------------------------------------gtgaatcgatttctcacatcttcgtctcat---agtttctcttggatcttgcgagCAGGACTTAATCGCTGCGGCAAGAGTTGCAGGCTGCGATGGACGAACTATCTCCGGCCGGATATAAAACGAGGCGGGATCACAGCCCAAGA--AGAGGTTCT-

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88746373|gb|DY530514.1|DY530514
EST:     CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAG                         GGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGAC-AATCTACCTC
genomic: CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAGgtcggaacca ... gcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAA-CTACCTC
EST: gi|91874168|gb|EB404125.1|EB404125
EST:     CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAG                         GGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCC
genomic: CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAGgtcggaacca ... gcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCC
EST: gi|76285013|gb|DV024581.1|DV024581
EST:     CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAG                         GGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCC
genomic: CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAGgtcggaacca ... gcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCC
EST: gi|71308073|gb|DR790252.1|DR790252
EST:     CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAG                         GGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCC
genomic: CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAGgtcggaacca ... gcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCC
EST: gi|91048016|gb|EB158434.1|EB158434
EST:     CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAG                         GGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCC
genomic: CATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAGgtcggaacca ... gcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 2 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 28

CTCAAGAAGGGGCCCTGGACGCCGGAGGAGGACAAGCTCCTCGTCGACTACATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAGgtcggaacca ... gcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

CTCAAGAAGGGGCCCTGGACGCCGGAGGAGGACAAGCTCCTCGTCGACTACATCCAGACCAACGGCCATGGCAGCTGGCGCCTGCTCCCCAAGCTCGCAGgtcggaacca ... gcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattgcaggcacacgcgcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT
                         atctaac  putative branch site (score: 1)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggaaccatccctctcttcttgcttccatttcttcttcgcggtttccacccacacgccgtcgtcttgttagttctgcagctgcctccctgccggcctcaaccatacggatacggctgtgatgcttctcgctcggattgcaggcacacgcgcggtctcatctaacccccattcgcggcgcatttgcagGGCTAAACCGGTGCGGCAAGAGCTGCCGACTGCGGTGGACGAACTACCTCCGGCCGGACATCAAGCGCGGGCCCTTCACATCCGAGGAGCAGAAGTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT